|
| Status |
Public on Apr 21, 2023 |
| Title |
RNA from liver from YoungHet3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT
tissue: liver
age (years): 0.5
mouseid: YoungHet3
|
| Treatment protocol |
Parabiosis was carried out as previously described (Zhang et al., 2021). Female C57Bl/6 mice were pre-screened to minimize body size differences, and were randomly assigned to parabiosis pairs. Isochronic pairs consisted of two 3-month-old or 20-month-old mice and heterochronic pairs consisted of one 3-month-old mouse and one 20-month-old mouse. Pairs were surgically attached and maintained for 3 months. Following 3 months of parabiosis, a subset of mice were euthanized for analysis and another subset were surgically separated. Fascia and skin were sutured closed following separation, and mice were allowed to recover for 2 months, after which they were for euthanized for analysis. Short-term parabiosis pairs were maintained for 1 month prior to euthanasia and tissue collection.
|
| Growth protocol |
This experiment was approved by the Duke University IACUC. C57Bl/6 mice were obtained from Jackson Laboratories and acclimated to our animal facility for at least 48 h before being subjected to any experimental manipulation. Aged C57Bl/6 mice for parabiosis experiments were obtained from the NIA aged rodent colony. Mice were maintained in a barrier facility in sterilized, ventilated cages and fed standard laboratory chow (LabDiet 5053) and reverse osmosis drinking water ad libitum and maintained on a 12h:12h light:dark cycle. Mice were generally housed socially. Mice were humanely euthanized at the conclusion of each experiment by CO2 exposure followed by cervical dislocation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from mouse tissues using the Ambion RNAqueous Total RNA Isolation Kit (Invitrogen). ~25 mg of solid tissue was used as starting material. Concentration of RNA samples was determined using the Qubit RNA HS assay kit (Invitrogen). Total RNA isolated as described above was checked for quality using an Agilent 2100 Bioanalyzer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Young heterochronic parabiosis
|
| Data processing |
Reads were mapped with STAR (version 2.5.2b) (Dobin et al., 2013)
Reads were counted via featureCounts (version 1.5) (Liao et al., 2014)
Data was passed through RLD transformation (Love et al., 2014)
Genes with |transformed normalized count| < 1 were filtered out
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each Sample
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Jul 10, 2023 |
| Contact name |
Jesse Poganik |
| Organization name |
Brigham and Women's Hospital, Harvard Medical School
|
| Department |
Medicine/Genetics
|
| Lab |
Gladyshev Lab
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE224378 |
Gene expression changes in mice induced by parabiosis and recovery [RNA-seq] |
| GSE224447 |
DNA methylation and gene expression changes in mice induced by parabiosis and recovery |
|
| Relations |
| BioSample |
SAMN33023097 |
| SRA |
SRX19261968 |
